8.4 How Does Vermicomposting Influence Functional
Diversity of Bacterial Communities from Dead Plant
Material?
Functional diversity includes the wide range of metabolic activities carried out by the
microorganisms in an ecosystem and can describe the way in which diverse microorganisms interact as a meta-organism to perform specific functions (Goswami et al.
2017). Assessing functional diversity is of high ecological importance because it can
influence both the ecosystem dynamics and functioning (Tilman 1999). In the
present chapter, the functional prediction of the fresh materials and the respective
vermicomposts was performed by using a gene-based computational tool known as
PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of
Unobserved States) that allows to computationally infer metagenome functional
contents from 16S rRNA gene sequences (Langille et al. 2013). Predicted
metagenomes were collapsed using the Kyoto Encyclopedia of Genes and Genomes
(KEGG) Pathway metadata (Kanehisa et al. 2019). Putative functional genes
involved in cellulose metabolism, hormone synthesis and antibiotic production,
which can be considered as a proxy for plant growth and development, were also
predicted using PICRUSt tool.
Overall, we detected significant predicted increases in genes classified only as
“metabolism” in KEGG functional hierarchies in all four vermicomposts in comparison with the respective fresh plant materials (Fig. 8.6a). The same pattern
emerged for specific genes related to cellulose metabolism (Fig. 8.6b). The degree
of such effect varied with the type of plant material, and lower gene abundances were
found in the distilled grape marc-derived vermicompost compared to the other three
vermicomposts (Fig. 8.6a, b). This indicates that the bacterial communities initially
contained in the parent materials had an influence on the metabolic functions in the
resulting vermicomposts. Indeed, previous works have underlined the importance of
the starting material for driving bacterial succession during vermicomposting
(Fernández-Gómez et al. 2010; Yakushev et al. 2011). Other factors shaping the
functional diversity of vermicompost microbiomes may include the earthworm
species and/or the vermicomposting procedure (Domínguez et al. 2019).
With regard to the genes involved in the synthesis of plant hormones, the
vermicomposts obtained from the raw grape marc and Scotch broom plant material
had higher abundances than the respective initial substrates (Fig. 8.6c). An increase
in the abundance of genes related to antibiotic production was also observed in the
vermicompost samples, except for the distilled grape marc (Fig. 8.6d). Generally
speaking, processing of dead plant material through vermicomposting resulted in
increases in specific metabolic processes potentially beneficial for plant growth and
development. Indeed, antibiotic production by beneficial bacteria has been proposed
as a plausible mechanism by which vermicompost addition may confer disease
136
M. Gómez-Brandón et al.
Diversity of Bacterial Communities from Dead Plant
Material?
Functional diversity includes the wide range of metabolic activities carried out by the
microorganisms in an ecosystem and can describe the way in which diverse microorganisms interact as a meta-organism to perform specific functions (Goswami et al.
2017). Assessing functional diversity is of high ecological importance because it can
influence both the ecosystem dynamics and functioning (Tilman 1999). In the
present chapter, the functional prediction of the fresh materials and the respective
vermicomposts was performed by using a gene-based computational tool known as
PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of
Unobserved States) that allows to computationally infer metagenome functional
contents from 16S rRNA gene sequences (Langille et al. 2013). Predicted
metagenomes were collapsed using the Kyoto Encyclopedia of Genes and Genomes
(KEGG) Pathway metadata (Kanehisa et al. 2019). Putative functional genes
involved in cellulose metabolism, hormone synthesis and antibiotic production,
which can be considered as a proxy for plant growth and development, were also
predicted using PICRUSt tool.
Overall, we detected significant predicted increases in genes classified only as
“metabolism” in KEGG functional hierarchies in all four vermicomposts in comparison with the respective fresh plant materials (Fig. 8.6a). The same pattern
emerged for specific genes related to cellulose metabolism (Fig. 8.6b). The degree
of such effect varied with the type of plant material, and lower gene abundances were
found in the distilled grape marc-derived vermicompost compared to the other three
vermicomposts (Fig. 8.6a, b). This indicates that the bacterial communities initially
contained in the parent materials had an influence on the metabolic functions in the
resulting vermicomposts. Indeed, previous works have underlined the importance of
the starting material for driving bacterial succession during vermicomposting
(Fernández-Gómez et al. 2010; Yakushev et al. 2011). Other factors shaping the
functional diversity of vermicompost microbiomes may include the earthworm
species and/or the vermicomposting procedure (Domínguez et al. 2019).
With regard to the genes involved in the synthesis of plant hormones, the
vermicomposts obtained from the raw grape marc and Scotch broom plant material
had higher abundances than the respective initial substrates (Fig. 8.6c). An increase
in the abundance of genes related to antibiotic production was also observed in the
vermicompost samples, except for the distilled grape marc (Fig. 8.6d). Generally
speaking, processing of dead plant material through vermicomposting resulted in
increases in specific metabolic processes potentially beneficial for plant growth and
development. Indeed, antibiotic production by beneficial bacteria has been proposed
as a plausible mechanism by which vermicompost addition may confer disease
136
M. Gómez-Brandón et al.